---
title: "Hands on 5-A_B: Trajectory Inference in R"
canonical: "https://help.biobam.com/space/BTP/3324051508/Hands%20on%205-A_B%3A%20Trajectory%20Inference%20in%20R"
format: markdown
---
This hands-on will have two parts. 

1. Fundamental Analysis will Monocle3.
2. Advance Object Handling and Differential Expression with Monocle3.


**Duration:** 60 min (30 + 30)


**A. Hands-on material for fundamental analysis will Monocle3:**

- Data and scripts: `HandsOn5_A_Monocle3_Trajectory_Analysis/input_data` folder
- Script: `hands-on-session5_A_Monocle3_Trajectory_Analysis.Rmd`
- Download the [RMarkdown](https://drive.google.com/file/d/1Jf-Y3ECfDwjOIbWfzvlYeB4zXOBo_sE8/view?usp=drive_link)
- [Link to the Data](https://drive.google.com/drive/folders/11EiuSRBwWVp4qZfVIeYo-oiniEz6J3xj?usp=sharing)
- [View the rendered document](https://metapriyansh.com/sdac_2023/5a.html) or [download the PDF](https://drive.google.com/file/d/1R9dNY6MbK1cmsPQg9qNzVLoV9QWSiK6o/view?usp=drive_link).


**B. Hands-on material for advanced analysis Monocle3:**

- Data and scripts: `HandsOn5_B_Trajectory_Analysis_Advance/input_data` folder
- Script: `hands-on-session5_B_Advanced_Procedures_for_Trajetcory_Analysis.Rmd`
- Download the [RMarkdown](https://drive.google.com/file/d/1-hDnP9MYBE_yF-Ps_csPevfSj6RR8pBm/view?usp=sharing)
- [Link to the Data](https://drive.google.com/drive/folders/1AaEV37lNHKuNag2L-0KPiOctkhtvcCBV?usp=sharing)
- [View the rendered document](https://metapriyansh.com/sdac_2023/5b.html) or [download the PDF](https://drive.google.com/file/d/1fz5at6__7arK-LBdq0iN5tB-tP97mAEi/view?usp=drive_link).

---

References and Useful links 

- [https://cole-trapnell-lab.github.io/monocle3/docs/getting_started/](https://cole-trapnell-lab.github.io/monocle3/docs/getting_started/)
- [https://cole-trapnell-lab.github.io/monocle3/docs/trajectories/](https://cole-trapnell-lab.github.io/monocle3/docs/trajectories/)